In order to study the impact of hydrological changes of the Amazon River on sedimentation process and organic matter (OM) accumulation, in an Amazonian floodplain lake during the Holocene, three sediment cores were collected from Quistococha Lake, Peru. The cores were dated with 14C accelerator mass spectrometry (AMS), radiographed, and described. Bulk density, granulometry, loss on ignition (LOI), total organic carbon (TOC) and total nitrogen (TN) contents were measured, and stable isotopic composition of TOC (δ13C) and TN (δ15N) and carbon accumulation rates were determined. Two distinctive sedimentary depositional phases were identified based on the lithology, granulometry and the geochemical characteristics of sedimentary OM. Between about 6100 and 4900calyears BP, the lake was under strong influence of the Amazon River. The river induced highest sedimentation rates (mean 0.5cmyr-1), a predominant deposition of relatively coarse particles (coarse silt), low LOI (1%), low contents of organic carbon (0.5%), low C/N ratios (~10), relatively low δ13C values (-26.0%), very laminated sediments and high carbon accumulation rates between 14 and 29gCm-2yr-1. A gap in the record between about 4900 and 2600calyears BP corresponds to a sedimentation hiatus during the dry mid Holocene. This gap is probably due to an avulsion of the main stem that induced significant changes in the lacustrine sedimentation. After 2600calyears BP, sedimentation resumed but now the lake was isolated far from the Amazon influence. The resumption of sedimentation corresponds to wetter conditions during the late Holocene and an increase in water levels. The lake was now characterized by very low sedimentation rates (0.02cmyr-1), fine organic-rich sediments with high LOI (between 20 and 80%), TOC (between 10 and 40% of TOC), high C/N ratio (20), and lower δ13C and δ15N indicating a predominant deposition of C3-plant derived OM. Carbon accumulation in this sedimentary depositional phase was about 8gCm-2yr-1. These results, combined with those of studies from other isolated lakes (Cordeiro et al., 1997, 2008; Turcq et al., 2002) and from other floodplain lakes (Moreira et al., 2012; Moreira et al., 2013), point out that floodplain lakes with strong influences from the Amazon River act as important carbon sinks in the Amazon Basin despite their low carbon concentrations.